User: kathryn.eckartt

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Posts by kathryn.eckartt

<prev • 6 results • page 1 of 1 • next >
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DESeq2 results versus by eye comparison in IGV
... Naive question but is it common for the fold change in gene expression for a locus to appear greater by eye in IGV than in the fold change calculated by DESeq2? For example, the log2FC of geneA is -1.667704322 ![IGV view of geneA][1] [1]: https://i.ibb.co/PQ0M86m/IGV-gene-A.png These tracks a ...
deseq2 rna-seq igv written 3 days ago by kathryn.eckartt20 • updated 2 days ago by shawn.w.foley710
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Comment: C: geneCounts from sorted bam all 0?
... Yuhp, that's correct- the reference doesn't have a gene-id. There isn't a Chromosome heading in the gff file, that is just what each line starts with. ...
written 11 weeks ago by kathryn.eckartt20
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Comment: C: geneCounts from sorted bam all 0?
... If I understand what you're asking, it's the gene_id that's common. The gff lists Chromosome name feature rank position strand ID and the reference genome for the single chromosome lists >Assembly_species_complete_genome TTAAGGGCCC After aligned, sorted bam ...
written 11 weeks ago by kathryn.eckartt20
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Comment: C: geneCounts from sorted bam all 0?
... Yuhp, they are both of the same organism from the same assembly. Since the organism is a bacteria and there is only 1 chromosome the gene_id is the common identifier between files. ...
written 11 weeks ago by kathryn.eckartt20
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geneCounts from sorted bam all 0?
... I appreciate any advice you could give! I'm using R version 3.4.4, platform 64-bit Linux-gnu. I've aligned RNAseq reads to a reference genome using QuasR and created a gene model from a GFF file: qAlign("sampleTable.txt","refGenome.fa,splicedAlignment=TRUE) library(GenomicFeatures) g ...
R bioconductor genomicfeatures rna-seq written 11 weeks ago by kathryn.eckartt20 • updated 11 weeks ago by zx87547.5k
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Understanding significance of enrichR results
... I have a set of differential expressed genes from RNAseq that I'm running basic enrichment analysis on using enrichR. How is one meant to interpret the combined score value in the resulting data frame? Should this be used to determine significance instead of the adjusted P value? I thought it migh ...
enrichr significance rna-seq statistics written 6 months ago by kathryn.eckartt20 • updated 6 months ago by Charles Warden6.8k

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